METHOD Stiff
 
STARTTIME = 0
STOPTIME=200
DT = 0.02
 
 
; Differential equations
d/dt(TCA)=0;
d/dt(PPP)=0;
d/dt(Glyc)=0; Glycolysis
d/dt(c1)=TCA+v1+v4+v10+v56+v54+v30+v22+v46+v25-v13;
d/dt(c2)=TCA+v50-2*v21-v27+v36-v55-v1;
d/dt(c3)=TCA+v43-v10;
d/dt(c4)=v20-v21;
d/dt(c5)=v33-v34-v48;
d/dt(c6)=v26-v27-v33;
d/dt(c7)=v11-v12;
d/dt(c8)=v34-v35;
d/dt(c9)=v35-v36;
d/dt(c10)=v36-v37-v38-v39;
d/dt(c11)=v21-v22;
d/dt(c12)=v55-v56-v23;
d/dt(c13)=v24-v25;
d/dt(c14)=v23-v24;
d/dt(c15)=v27-v28;
d/dt(c16)=v28-v29; 
d/dt(c17)=v29-v30;
d/dt(c18)=v30-v31;
d/dt(c19)=v31-v32;
d/dt(c20)=v3-v6;
d/dt(c21)=v2-v4; 
d/dt(c22)=v4-v5; 
d/dt(c23)=v6-v7;
d/dt(c24)=v7-v8;
d/dt(c25)=PPP*0.26-v51-v17;
d/dt(c26)=v17-v18;
d/dt(c27)=v18-v19;
d/dt(c28)=PPP-v40;
d/dt(c29)=TCA*0.18-v41-v40;
d/dt(c30)=v40-v41;
d/dt(c31)=v41-v49;
d/dt(c32)=v49-v50-v42;
d/dt(c33)=v42-v43-v53;
d/dt(c34)=v53-v54; 
d/dt(c35)=v50-v51;
d/dt(c36)=v51-v52
d/dt(c37)=v5-v6;
d/dt(c38)=v1-vprot2*0.067; 
d/dt(c39)=v8-vprot2*0.092;
d/dt(c40)=v9-vprot2*0.073;
d/dt(c41)=v10-v26-v43-v9-v7-vprot2*0.088;
d/dt(c42)=v12-v35-vprot2*0.006;
d/dt(c43)=v13+v14-v15+v17-v1-v2-v3-v4-v22-v30-v44-v54-v56+v50+v9-v10-v46-v54-v25-vprot2*0.085;
d/dt(c44)=v15-v14-v17-v50-v9-vprot2*0.073;
d/dt(c45)=v16-vprot2*0.073;
d/dt(c46)=v19-vprot2*0.017;
d/dt(c47)=v22-vprot2*0.031;
d/dt(c48)=v25-vprot2*0.06;
d/dt(c49)=v32-vprot2*0.046;
d/dt(c50)=v39+v38+v37-vprot2*0.015*0.001;  
d/dt(c51)=v43-vprot2*0.017;
d/dt(c52)=v44-vprot2*0.073;
d/dt(c53)=v46-v52-v11-v16;-vprot2*0.094-c53*k;
d/dt(c54)=v48-v20;-vprot2*0.023;
d/dt(c55)=v52-vprot2*0.006;
d/dt(c56)=v54-vprot2*0.023;
d/dt(c57)=v56-vprot2*0.04;
d/dt(c58)=0;Glyc*9.6-v2-v3-v7-v9-v15-v17-v26-v40-v48;
d/dt(c59)=0;Glyc*0.56+v2+v3+v15+v26+v40+v48;
d/dt(c60)=0;Glyc*0.28+v7+v9;
d/dt(c61)=0;Glyc*(0.12+0.083)-v2+v3-v13+4*v19+v24-v26-v28-v33-v40-2*v44-v55+v53+v21+v45;
d/dt(c62)=0;Glyc*(2.6+0.0021)+v2-v3+v13-4*v19-v24+v26+v28+v33+v40+2*v44+v55-v53-v21-v45;
d/dt(c63)=0;PPP*0.27+v17; Concentration not found for AICAR, so instead found for inosine-monophosphate
d/dt(c64)=0;Glyc*0.61-v2-v11-v23;
d/dt(c65)=0;Glyc*1.4+v2+v11+v29+v34+v23;
d/dt(c66)=0;Glyc+v5+v12; Normal conc. of acetate in cells could not be found
d/dt(c67)=0;TCA*0.23-v29-v34;
d/dt(c68)=0;TCA*0.57+v31+v35;
d/dt(c69)=0;TCA-v12; What pathway? and cell concentration could not be found
d/dt(c70)=0;v2+v6+2*v7+2*v9+v15+2*v17+v19+v26+2*v40+v41+v48+2*v51; Could not find in pathway
d/dt(c71)=0;TCA-v13-v14-v15+v36; -v45-v46, What pathway?
d/dt(c72)=TCA*1.5-v45;
d/dt(c73)=v45-v46;
d/dt(ex1)=0; v52;
d/dt(ex2)=0; -v16;
d/dt(ex3)=0; v16;
d/dt(ex5)=0; v8;
d/dt(ex6)=0; -v37;
d/dt(ex7)=0; -v38;
d/dt(ex8)=0; v38;
d/dt(ex9)=0; -v39;
d/dt(ex10)=0; v39;
d/dt(Prot)=vprot2;

vprot2=PP*(c38/(c38+1))*(c39/(c39+1))*(c40/(c40+1))*(c41/(c41+1))*(c42/(c42+1))*(c43/(c43+1))*(c44/(c44+1))*(c45/(c45+1))*(c46/(c46+1))*(c47/(c47+1))*(c48/(c48+1))*(c49/(c49+1))*(c50/(c50+1))*(c51/(c51+1))*(c52/(c52+1))*(c53/(c53+1))*(c54/(c54+1))*(c55/(c55+1))*(c56/(c56+1))*(c57/(c57+1));
PP=10000;
 
; Enzyme rate terms

; EC 2.6.1.2 (Pyruvat + Glutamat <lt>-<gt> Alanin + 2-oxoglutarate)
v1=(Vmax1f*c2/km1c2*c43/km1c43-Vmax1r*c38/km1c38*c1/km1c1)/(1+c2/km1c2+c43/km1c43+c2/km1c2*c43/km1c43+c38/km1c38+c1/km1c1+c38/km1c38*c1/km1c1);
Vmax1f=0.17; Forward Vmax, value used for Pseudomonas putida
Vmax1r=0.08; Reverse Vmax, value used for Pseudomonas putida
km1c2=0.2; Value used for Pseudomonas putida
km1c43=0.57; Value used for Pseudomonas putida
km1c38=0.21; Value used for Pseudomonas putida
km1c1=0.05; Value used for Pseudomonas putida
 
; EC 2.7.2.8 (Glutamat -<gt> N-acetyl-glutamat semialdehyd)
v2=(Vmax2*c43*c61*c58*c64)/(km2+c43*c61*c58*c64);
Vmax2=80;
km2=1.3;

; EC 1.4.1.4 (Glutamat -<gt> Carbamoyl-P)
v3=(Vmax3*c43*c58*c62)/(km3+c43*c58*c62);
Vmax3=37.9;
km3=2.3;

; EC 2.6.1.11 (N-acetyl-glutamat semialdehyd -<gt> N-acetyl ornithine)
v4=(Vmax4*c21*c43)/(km4c21*km4c43+c21*km4c43+c43*km4c21+c21*c43);
Vmax4=670; Values from enzyme EC 2.6.1.1 - v54 used for Vmax and km values
km4c21=15;
km4c43=37;

; EC 3.5.1.16 (N-acetyl ornithine -<gt> L-ornithine)
v5=(Vmax5*c22)/(km5+c22);
Vmax5=1600;
km5=1.56;

; EC 2.1.3.3 (Carbamoyl-P + L-ornitine -<gt> Citruline)
v6=(Vmax6*c20*c37)/(km6c20*km6c37+c20*km6c37+c37*km6c20+c20*c37);
Vmax6=5146.6;
km6c20=0.36;
km6c37=0.85;

; EC 6.3.4.5 (Citruline + Aspartat -<gt> L-argino-succinat)
v7=(Vmax7*c23*c41*c58)/(km7c23*km7c41+c23*c58*km7c41+c41*c58*km7c23+c23*c41*c58);
Vmax7=0.183;
km7c23=0.056; Used value from Homo Sapiens
km7c41=0.027; Used value from Homo Sapiens

; EC 4.3.2.1 (L-argino-succinat -<gt> Arginin)
v8=(Vmax8*c24)/(km8+c24);
Vmax8=4.9; Used value from Anas platyrhynchos (Duck)
km8=0.26; Used value from Chlamydomonas reinhardtii (Algae)

; EC 6.3.5.4 (Asp + Gln <lt>-<gt> Glu + Asn)
v9=Vmax9*c41*c44*c58/(km9c41*km9c44+c41*c58*km9c44+c44*c58*km9c41+c41*c44*c58); It is assumed that the reaction is irreversible
Vmax9=0.57; Between 0.57-1.05
km9c41=0.85;
km9c44=0.69; Between 0.6-0.69

; EC 2.6.1.1 (Oxaloacetate + L-Glutamat <lt>-<gt> Aspartat + 2-oxoglutarate)
v10=(Vmax10c3c43*c3/km10c3*c43/km10c43-Vmax10c41c1*c41/km10c41*c1/km10c1)/(1+c3/km10c3+c43/km10c43+c3/km10c3*c43/km10c43+c41/km10c41+c1/km10c1+c41/km10c41*c1/km10c1)
km10c3=0.37; pH 7.6, 25 degree Celsius
km10c43=0.09; 37; pH 7.5, 25 degree Celsius, wild-type
km10c41=4; pH 7.5, 25 degree Celsius, wild-type
km10c1=0.071; pH7.6, 25 degree Celsius
Vmax10c3c43=18; Used kcat for glutamat since it was the lowest
Vmax10c41c1=133; Used kcat for aspartat since it was the lowest

; EC 2.3.1.30 (Serin <lt>-<gt> O-acetyl-L-serin)
v11=Vmax11*c53*c64/((km11+c53*c64)*(1+c42/ki11)); It is assumed that the reaction is irreversible. The reaction exhibits non-competitive inhibition by cystein.
Vmax11=0.068;
km11=0.11;
ki11=0.0006;

; EC 2.5.1.47 (O-acetyl-L-serine -<gt> Cystein) Competitive inhibition by Cystein
v12=Vmax12*c7*c69/(km12+c7*c69+km12*c42/ki12);
Vmax12=24; Between 24-733
km12=1.3; Between 0.7-1.3
ki12=8.6;

; EC 1.4.1.13 (2-oxoglutarat -<gt> Glutamat)
v13=(Vmax13*c1*c61*c71)/(km13+c1*c61*c71);
Vmax13=12.40; 
km13=0.24;
 
; EC 3.5.1.2 (Glutamat <lt>-<gt> Glutamin)
v14=((Vmax14c44*c44)/km14c44-(Vmax14c43*c43*c71)/km14c43)/(1+c44/km14c44+c43*c71/km14c43);
km14c44=7.3; Between 7.3-30.6
km14c43=0.42; Between 0.42-2.9
Vmax14c44=91.4; Between 91.4-101
Vmax14c43=1270; Between 1270-5080

;  EC 6.3.1.2 (Glutamat -<gt> Glutamin)
v15=(Vmax15*c43*c58*c71)/(Km15+c43*c58*c71);
Vmax15=27; Between 27-40
Km15=3.3;

; EC 2.1.2.1 (Ser + Tetrahydrofolate <lt>-<gt> 5,10-methylenetetrahydrofolate + Gly)
v16=(Vmax16f*(c53/km16c53)*(ex2/km16ex2)-Vmax16r*(c45/km16c45)*(ex3/km16ex3))/(1+(c53/km16c53)+(ex2/km16ex2)+(c53/km16c53)*(ex2/km16ex2)+(c45/km16c45)+(ex3/km16ex3)+(c45/km16c45)*(ex3/km16ex3));
Vmax16f=450;640;
Vmax16r=580;640;
km16c53=0.519;0.3;
km16ex2=0.015; Between 0.00703-0.015
km16c45=0.3;
km16ex3=0.015;

; hisFH (PRPP + Gln -<gt> Imidazole Glycerol 3-phosphat + Glu)
v17=Vmax17*c25*c44*c58/(km17c25*km17c44+c25*c58*km17c44+c44*c58*km17c25+c25*c58*c44);
Vmax17=8.5; Value obtained from [Demin, O. V. et. al. 2004]
km17c25=0.0015; Value obtained from [Demin, O. V. et. al. 2004]
km17c44=0.24; Value obtained from [Demin, O. V. et. al. 2004]

; EC 2.6.1.9 (Imidazole glycerol-3-P <lt>-<gt> L-histidinol-P)
v18=(Vmax18f*c26/km18c26-Vmax18r*c27/km18c27)/(1+c26/km18c26+c27/km18c27);
Vmax18f=1; Arbitrary value, adjust so it does not influence
Vmax18r=1; Arbitrary value, adjust so it does not influence
km18c26=1; Arbitrary value, adjust so it does not influence
km18c27=1; Arbitrary value, adjust so it does not influence

; EC 3.1.3.15 (L-Histidinol-3-phosphat -<gt> Histidin)
v19=Vmax19*c27*0.25*c62/(km19+c27*0.25*c62); Multiplied by 0.25 since 4 NAD are required pr. c27
Vmax19=960;
km19=0.041;

; EC 4.3.1.19 (Thr -<gt> 2-oxobutanoat)
v20=Vmax20*c54/(km20+c54);
Vmax20=150.36; Value calculated from the specific activity and molecular weight of enzyme
km20=11;

; EC 2.2.1.6 (Pyruvate + 2-oxobutanoat -<gt> (S)-3-methyl-2-oxopentanoat)
v21=Vmax21*c62*c2*c4/(km21c2*km21c4+c2*km21c4+km21c2*c4+c2*c4);
Vmax21=23.3; Between 23.3-71
km21c2=6.6; Between 2.6-6.6
km21c4=5; Between 1-5

; EC 2.6.1.42 ((S)-3-methyl-2-oxopentanoate + Glu -<gt> 2-oxoglutarate + Ile)
v22=Vmax22*c11*c43/(km22c11*km22c43+c11*km22c43+c43*km22c11+c11*c43);
Vmax22=48;
km22c11=0.2;
km22c43=9.53; Value obtained from  Mycobacterium tuberculosis

; EC 2.3.3.13 (2-oxoisovalerate -<gt> 2s-2-isopropylmalate)
v23=Vmax23*c12*c64/(km23+c12*c64);
Vmax23=0.77; Between 0.77-3.5, Value obtained from  Mycobacterium tuberculosis
km23=0.0246; Between 0.0017-0.0246, Value obtained from  Mycobacterium tuberculosis

; EC 1.1.1.85 ((2S)-2-isopropylmalate)
v24=Vmax24*c14*c62/(km24+c14*c62);
Vmax24=69;
km24=0.321;

; EC 2.6.1.42 (4-methyl-2-oxopentanoat + Glu <lt>-<gt> 2-oxoglutarate + Leucin)
v25=(Vmax25f*c13/km25c13*c43/km25c43-Vmax25r*c48/km25c48*c1/km25c1)/(1+c13/km25c13+c43/km25c43+c13/km25c13*c43/km25c43+c48/km25c48+c1/km25c1+c48/km25c48*c1/km25c1);
Vmax25f=6.61; Forward Vmax
Vmax25r=78; Reverse Vmax
km25c13=0.76;
km25c43=25; Between 18.2-25
km25c48=2.2; Between 0.58-2.2
km25c1=6.6;

; EC 2.7.2.4 (Aspartat -<gt> L-aspartat-4-semialdehyd)
v26=(Vmax26*c41*c58*c61)/(km26+c41*c58*c61);
Vmax26=2.22; 0.39;
km26=0.63;

; EC 4.3.3.7 (L-aspartat-4-semialdehyd + pyruvat -<gt> (2S4S)-4-hydroxy-2,3,4,5-tetra-hydroxy-dipicolinat)
v27=(Vmax27*c6*c2)/(km27c6*km27c2+c6*km27c2+c2*km27c6+c6*c2)
Vmax27=9.8; Between 9.8-223
km27c6=0.13; Between 0.13-0.14
km27c2=0.16; Between 0.16-0.26

; EC 1.17.1.8 ((2S4S)-4-hydroxy-2,3,4,5-tetra-hydroxy-dipicolinat -<gt> L-2,3,4,5-tetra-hydrodipicolinate)
v28=(Vmax28*c15*c61)/(km28+c15*c61);
Vmax28=20; Used value from Staphylococcus aureus
km28=0.529;

; EC 2.3.1.117 (L-2,3,4,5-tetra-hydrodipicolinate -<gt> N-succinyl-L-2-amino 6-oxopimelate)
v29=(Vmax29*c16*c67)/(km29+c16*c67);
Vmax29=43.2;
km29=0.02; Between 0.02-0.022

; EC 2.6.1.17 (N-succinyl-L-2-amino 6-oxopimelate + Glu <lt>-<gt> 2-oxoglutamat + N-succinyl-LL-2.8-diamino pimelate)
v30=(Vmax30*c17*c43)/(km30c17*km30c43+c17*km30c43+c43*km30c17+c17*c43); It is assumed that the reaction is irreversible
Vmax30=7.28; Value calculated from the specific activity
km30c17=0.18;
km30c43=1.21;

; EC 3.5.1.18 (N-succinyl-LL-2.8-diamino pimelate -<gt> LL-2,6-diamino pimelate)
v31=(Vmax31*c18)/(km31+c18);
Vmax31=140; Used value from Haemophilus influenzae
km31=1.3;

; EC 4.1.1.20 (LL-2,6-diamino pimelate -<gt> Lysin)
v32=(Vmax32*c19)/(km32+c19);
Vmax32=25;
km32=1.7; Vmax calculated from specific activity of enzyme

; EC 1.1.1.3 (L-aspartat-4-semialdehyde <lt>-<gt> Homoserin)
v33=(Vmax33f*c6*c61/km33c6-Vmax33r*c5*c62/km33c5)/(1+c6*c61/km33c6+c5*c62/km33c5);
Vmax33f=2.8; Forward Vmax, value used from Glycine Max (Soy beans)
Vmax33r=0.24; Reverse Vmax, value used from Glycine Max (Soy beans)
km33c6=0.01; 0.17;
km33c5=0.013;

; EC 2.3.1.46 (Homoserin -<gt> O-succinyl-L-homoserin)
v34=(Vmax34*c5*c67)/(km34+c5*c67);
Vmax34=24;
km34=0.38;

; EC 2.5.1.48 (O-succinyl-L-homoserin -<gt> L-cystathionin)
v35=Vmax35*c8*c42/(km35c8*km35c42+c8*km35c42+c42*km35c8+c8*c42);
Vmax35=18; Between 18-117
km35c8=4.4; Between 1.3-4.4
km35c42=0.24;

; EC 4.4.1.8 (L-cystathionin -<gt> L-homocystein + Pyruvate)
v36=(Vmax36*c9)/(km36+c9);
Vmax36=34.1;
km36=0.18; Between 0.04-0.18

; EC 2.1.1.10 (L-homocystein + S-methyl-L-methionin -<gt> Methionin)
v37=(Vmax37*c10*ex6)/(km37c10*km37ex6+c10*km37ex6+km37c10*ex6+c10*ex6);
Vmax37=0.38;
km37c10=0.045;
km37ex6=1.95; Between 0.029-1.95, Value used is from Arabidopsis thaliana

; EC 2.1.1.14 (L-homocystein + 5-methyltetrahydropteroyltri-L-glutamat -<gt> Methionin + tetrahydropteroyltri-L-glutamat)
v38=(Vmax38*c10*ex7)/(km38c10*km38ex7+c10*km38ex7+ex7*km38c10+c10*ex7);
Vmax38=0.12;
km38c10=0.69;
km38ex7=0.0044;

; EC 2.1.1.13 (L-homocystein + 5-methyltetrahydrofalat -<gt> Methionin + tetrahydrofalat)
v39=(Vmax39*c10*ex9)/(km39c10*km39ex9+c10*km39ex9+ex9*km39c10+c10*ex9);
Vmax39=8.33;
km39c10=0.069; Between 0.016-0.069
km39ex9=0.03;

; EC 2.5.1.54 (D-erytrose-4-phosphat + Phosphoenolpyruvat -<gt> Shikimate-3-phosphate) Exhibits non-competitive inhibition by Tyr.
v40=Vmax40*c28*c29*c58*c61/((km40c28*km40c29+c28*c58*c61*km40c29+c29*c58*c61*km40c28+c28*c29*c58*c61)*(1+c56/ki40));
Vmax40=122;
km40c28=0.9;
km40c29=0.08;
ki40=0.02;

; EC 2.5.1.19 (Shikimate-3-phosphate + Phosphoenolpyruvate -<gt> 5-O-(1-carboxyvinyl)-3-phosphate)
v41=Vmax41*c30*c29/(km41c30*km41c29+c30*km41c29+c29*km41c30+c30*c29);
Vmax41=26.4;
km41c30=0.135; Between 0.048-0.135
km41c29=0.1; Between 0.045-0.1

; EC 5.4.99.5 (Chorismate <lt>-<gt> Prephenate)
v42=(Vmax42f*c32/km42c32-Vmax42r*c33/km42c33)/(1+c32/km42c32+c33/km42c33);
Vmax42f=140500; Forward Vmax
Vmax42r=94100; Reverse Vmax
km42c32=0.3;
km42c33=0.47;

; EC 2.6.1.57 (Prephenate + Asp -<gt> Phe + oxaloacetat)
v43=Vmax43*c33*c41/(km43c33*km43c41+c33*km43c41+c41*km43c33+c33*c41);
Vmax43=290;
km43c33=0.056;
km43c41=5;

; EC 1.5.1.2 (Glutamat -<gt> Prolin)
v44=(Vmax44*c43*0.5*c61)/(km44+c43*0.5*c61); Multiplied by 0.5 since two NADH are required pr. Glu
km44=0.14; Between 0.14-0.15
Vmax44=84.8;

; EC 1.1.1.95 (3P-D-Glycerate <lt>-<gt> 3P-hydroxypyruvate)
v45=(Vmax45f*c72*c62/km45c72-Vmax45r*c73*c61/km45c73)/(1+c72*c62/km45c72+c73*c61/km45c73);
Vmax45f=13.5;
Vmax45r=0.463;
km45c72=0.49;
km45c73=0.0032; Between 0.0013-0.0032

; EC 2.6.1.52 (3P-hydroxypyruvate + Glu <lt>-<gt> 2-oxoglutarate + Ser)
v46=(Vmax46f*c73/km46c73*c43/km46c43-Vmax46r*c53*c70/km46c53*c1/km46c1)/(1+c73/km46c73+c43/km46c43+c73/km46c73*c43/km46c43+c53*c70/km46c53+c1/km46c1+c53*c70/km46c53*c1/km46c1);
Vmax46f=5.005; Between 1.33-1.75. Value is adjusted
Vmax46r=0.39; Between 0.39-0.63
km46c73=0.01; Between 0.015-0.01;
km46c43=0.007; Value is from Entamoeba histolytica. Value is adjusted from 0.788
km46c53=0.037; Between 0.017-0.037
km46c1=0.043; Value is from Entamoeba histolytica

; EC 2.7.1.39 (Homoserin -<gt> Threonin) Non-competitive inhibition by Thr
v48=Vmax48*c5*c58/((km48+c5*c58)*(1+c54/ki48));
Vmax48=18.3;
km48=6.9; Between 0.14-6.9
ki48=0.3;

; EC 4.2.3.5 (5-O-(1-carboxyvinyl)3-phosphate -<gt> Chorismate)
v49=Vmax49*c31/(km49+c31);
Vmax49=35.52; Calculated from the specific activity
km49=0.0013;

; EC 4.1.3.27 (Chorismate + Gln -<gt> Pyruvat + Glu + Antranilat)
v50=Vmax50*c32*c44/(km50c32*km50c44+c32*km50c44+c44*km50c32+c32*c44);
Vmax50=2.6; Calculated from specific activity
km50c32=0.029;
km50c44=0.36;

; EC 2.4.2.18 (Antranilat + PRPP -<gt> N-(5-phospho-D-ribosyl)antranilat)
v51=Vmax51*c35*c25/(km51c35*km51c25+c35*km51c25+c25*km51c35+c35*c25);
Vmax51=0.35;
km51c35=0.000085;
km51c25=1.54;

; EC 4.2.1.20 (N-(5-phospho-D-ribosyl)antranilat + Serin -<gt> Tryptophan + Glyceraldehyde-3-phosphat)
v52=Vmax52*c36*c53/(km52c36*km52c53+c36*km52c53+c53*km52c36+c36*c53);
Vmax52=305.21; Calculated from specific activity
km52c36=0.032; Value used is from S. Cerevisae
km52c53=0.98; Value used is from Salmonella enterica subsp. enterica serovar Typhimurium

; EC 1.3.1.12 (Prephenate -<gt> 3-(4-hydroxyphenyl)-pyruvat)
v53=Vmax53*c33*c62/(km53+c33*c62);
Vmax53=135;
km53=0.37; Between 0.045-0.37

; EC 2.6.1.1 (3-(4-hydroxyphenyl)-pyruvat + Glu -<gt> 2-oxoglutarate + Tyr)
v54=Vmax54*c34*c43/(km54c34*km54c43+c34*km54c43+c43*km54c34+c34*c43);
Vmax54=670;
km54c34=15;
km54c43=37;

; EC 2.2.1.6 (Pyruvat -<gt> 2-oxoisovalerate)
v55=Vmax55*c2*c61/(km55+c2*c61);
Vmax55=23.3; Between 23.3-71
km55=6.6; Between 4.8-6.6

; EC 2.6.1.42 (2-oxoisovalerate + Glu -<gt> 2-oxoglutarat + Val)
v56=Vmax56*c12*c43/(km56c12*km56c43+c12*km56c43+c43*km56c12+c12*c43);
Vmax56=16.84;
km56c12=0.56;
km56c43=3.2;Value used found from Pseudomonas sp.


; Initial values
init TCA=1;
init PPP=1;
init Glyc=1;
init c1=1;
init c2=1;
init c3=1;
init c4=1;
init c5=1;
init c6=1;
init c7=1;
init c8=1;
init c9=1;
init c10=1;
init c11=1;
init c12=1;
init c13=1;
init c14=1;
init c15=1;
init c16=1;
init c17=1;
init c18=1;
init c19=1;
init c20=1;
init c21=1;
init c22=1;
init c23=1;
init c24=1;
init c25=1;
init c26=1;
init c27=1;
init c28=1;
init c29=1;
init c30=1;
init c31=1;
init c32=1;
init c33=1;
init c34=1;
init c35=1;
init c36=1;
init c37=1;
init c38=1;
init c39=1;
init c40=1;
init c41=1;
init c42=1;
init c43=1;
init c44=1;
init c45=1;
init c46=1;
init c47=1;
init c48=1;
init c49=1;
init c50=1;
init c51=1;
init c52=1;
init c53=1;
init c54=1;
init c55=1;
init c57=1;
init c56=1;
init c58=9.6;
init c59=0.56;
init c60=0.28;
init c61=(0.12+0.083);
init c62=(2.6+0.0021);
init c63=0.27;
init c64=0.61;
init c65=1.4;
init c66=1;
init c67=0.23;
init c68=0.57;
init c69=1;
init c70=1;
init c71=1;
init c72=1.5;
init c73=1;
init ex1=1;
init ex2=1;
init ex3=1;
init ex5=1;
init ex6=1;
init ex7=1;
init ex8=1;
init ex9=1;
init ex10=1;
init Prot=1;
init test=0;
